The gas-phase deprotonation reactions of multiply protonated ubiquitin ions have been studied in a Fourier-transform ion cyclotron resonance mass spectrometer. Electrospray ionization was used to generate ubiquitin ions with attachment of 7–13 protons. Rate constants were measured for the reactions of these protein ions with four amines: n-propylamine, di-n-propylamine, tri-n-propylamine, and N,N,N′,N′-tetramethyl-1,4-diaminobutane. The gas-phase basicities of the amines ranged from 210.1 kcal/mol to 232.6 kcal/mol. The rate constants were found to increase as the charge state of the ion increased and as the basicity of the amine increased. Several reactions proceed at near the collision rate and have rate constants in excess of 10−8 cm3 molecule−1 s−1. With the more basic reactants, multiple protons could be stripped sequentially from ubiquitin ions at roughly equivalent rates, suggsting that these protons are attached to sites with similar basicities. In general, deprotonation occurs if the gas-phase basicity of the amine is within 10 kcal/mol of the intrinsic gas-phase basicity of the amino acid residue being deprotonated. For [M+nH]n + , n = 4–6, nonlinear pseudo-first-order kinetic behavior indicated the presence of multiple ion structures. Kinetic, structural and thermodynamic aspects of these reactions are discussed.